[gmx-users] Re: improper dihedral angle in charmm and opls aa (Mark Abraham)
Tom
dnaafm at gmail.com
Sat Feb 11 23:22:21 CET 2012
Dear Mark and Gromacs Users,
Can you be more specific in explanation about improper dihedral of charmm
in gromacs?
For opls aa, it is very clear that every item of improper dihedral angle is
described once
on the *rtp file.
I am quite confused about the one in the charmm.
Ihe same angle is sometimes described twice despite of the difference in
the atoms' sequence.
Suposed for an unkown molecule, how to assign them on rtp file?
Can you give some introduction or show somewhere that has the document?
Gromacs menu does not document about this.
Thanks for advance!
Tom
>
> Message: 1
> Date: Sat, 11 Feb 2012 11:15:04 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] improper dihedral angle in charmm and opls aa
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4F35B308.3080504 at anu.edu.au>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On 11/02/2012 9:54 AM, Tom wrote:
> > Dear Gromacs Users
> > I am confused about definition of improper dihedral angle in charmm27,
> > which is compared to oplsaa.
> > Why charmm ff in gromacs give *double* items for the same dihedral angle.
> > e.g. for charmm27 ASN
> > CG ND2 CB OD1
> > CG CB ND2 OD1
> > ND2 CG HD21 HD22
> > ND2 CG HD22 HD21
>
> These are not duplicates. Atom ordering is significant. These *improper*
> dihedral angles are enforcing planarity of the amide moiety. This is
> done by influencing dihedral angles along intra-atom vectors where there
> is no bond. OPLS/AA is working differently somehow.
>
> Mark
>
> > in opls aa for ASN
> > CG CB CA C dih_ASN_chi1_C_C_C_CO
> > CA CB CG ND2 dih_ASN_chi2_C_C_CO_N
> > Thanks for advance!
> > Tom
> > PS:
> > the detail is as follows
> > ------------------------------------------------
> > *in charmm27.ff/aminoacids.rtp*
> > [ ASN ]
> > [ atoms ]
> > N NH1 -0.47 0
> > HN H 0.31 1
> > CA CT1 0.07 2
> > HA HB 0.09 3
> > CB CT2 -0.18 4
> > HB1 HA 0.09 5
> > HB2 HA 0.09 6
> > CG CC 0.55 7
> > OD1 O -0.55 8
> > ND2 NH2 -0.62 9
> > HD21 H 0.32 10
> > HD22 H 0.30 11
> > C C 0.51 12
> > O O -0.51 13
> > [ bonds ]
> > CB CA
> > CG CB
> > ND2 CG
> > N HN
> > N CA
> > C CA
> > C +N
> > CA HA
> > CB HB1
> > CB HB2
> > ND2 HD21
> > ND2 HD22
> > C O
> > CG OD1
> > [ impropers ]
> > N -C CA HN
> > C CA +N O
> > CG ND2 CB OD1
> > CG CB ND2 OD1
> > ND2 CG HD21 HD22
> > ND2 CG HD22 HD21
> > [ cmap ]
> > -C N CA C +N
> > -------------------------------------------
> > in*oplsaa.ff/aminoacids.rtp*
> > [ ASN ]
> > [ atoms ]
> > N opls_238 -0.500 0
> > H opls_241 0.300 0
> > CA opls_224B 0.140 1
> > HA opls_140 0.060 1
> > CB opls_136 -0.120 2
> > HB1 opls_140 0.060 2
> > HB2 opls_140 0.060 2
> > CG opls_235 0.500 3
> > OD1 opls_236 -0.500 3
> > ND2 opls_237 -0.760 4
> > HD21 opls_240 0.380 4
> > HD22 opls_240 0.380 4
> > C opls_235 0.500 5
> > O opls_236 -0.500 5
> > [ bonds ]
> > N H
> > N CA
> > CA HA
> > CA CB
> > CA C
> > CB HB1
> > CB HB2
> > CB CG
> > CG OD1
> > CG ND2
> > ND2 HD21
> > ND2 HD22
> > C O
> > -C N
> > [ dihedrals ] ; override some with residue-specific ones
> > N CA CB CG dih_ASN_chi1_N_C_C_C
> > CG CB CA C dih_ASN_chi1_C_C_C_CO
> > CA CB CG ND2 dih_ASN_chi2_C_C_CO_N
> >
> >
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20120211/a4d6d18e/attachment-0001.html
>
> ------------------------------
>
> Message: 2
> Date: Fri, 10 Feb 2012 16:22:18 -0800 (PST)
> From: MPID <mpmcgovern at wisc.edu>
> Subject: [gmx-users] g_wham with cylinder geometry
> To: gmx-users at gromacs.org
> Message-ID: <1328919738939-4385053.post at n6.nabble.com>
> Content-Type: text/plain; charset=us-ascii
>
> Hi everyone. I ran an umbrella sampling simulation of a protein in a
> membrane. I used pull_geometry=cylinder. I tried to analyze the results
> with
> g_wham. I got this error:
>
> Fatal error:
> With pull geometry 'cylinder', expected pulling in Z direction only.
> However, found dimensions [Y Y Y]
>
> The manual says that with this geometry the pulling is in the direction of
> pull_vec. I set pull_vec to 0 0 1. Do I have to redo these simulations with
> a line that says pull_dim = N N Y? Or does the data still mean what it is
> supposed to, but g_wham is just giving trouble and I can use a different
> wham program?
>
> Here is the pull part of my mdp file:
>
> pull = umbrella
> pull_geometry = cylinder
> pull_r0 = 2.0
> pull_r1 = 1.5
> pull_vec1 = 0 0 1
> pull_start = yes
> pull_group0 = DPPGB
> pull_group1 = PROT
> pull_k1 = 500
> pull_nstxout = 1000
> pull_nstfout = 1000
>
>
> --
> View this message in context:
> http://gromacs-users-forum.5086.n6.nabble.com/g-wham-with-cylinder-geometry-tp4385053p4385053.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>
>
> ------------------------------
>
> --
> gmx-users mailing list
> gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>
> End of gmx-users Digest, Vol 94, Issue 67
> *****************************************
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120211/3dff38b5/attachment.html>
More information about the gromacs.org_gmx-users
mailing list